If you want to compare executable files, you have a couple of alternatives:
- Bindiff: it's a commercial extension for the commercial disassembler IDA Pro. It's a de-facto tool for reverse engineering. According to the vendor description, it allows you to:
- Identify identical and similar functions in different binaries
- Port function names, anterior and posterior comment lines, standard comments and local names from one disassembly to the other
- Detect & highlight changes between two variants of the same function
http://www.zynamics.com/bindiff.html
- You still have a free alternative: PatchDiff. As Bindiff, it's also a plugin for IDA Pro. According to the developer, Patchdiff can perform the following tasks:
- Display the list of identical functions
- Display the list of matched functions
- Display the list of unmatched functions (with the CRC)
- Display a flow graph for identical and matched functions
http://cgi.tenablesecurity.com/tenable/patchdiff.php